GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas fluorescens GW456-L13

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD

Query= uniprot:A0A159ZWS6
         (255 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Urea ABC
           transporter, ATPase protein UrtD
          Length = 290

 Score =  157 bits (396), Expect = 3e-43
 Identities = 95/251 (37%), Positives = 151/251 (60%), Gaps = 12/251 (4%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           IL +E++S+ F G  A+N + L +   ++  +IGPNGAGKTT+ + +TG  +P+ G    
Sbjct: 49  ILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 108

Query: 65  DGEPIQ--GLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPA 122
            GE +    +    IA+ G+ R FQ   +F+ ++  ENL +AQ    + + +A L    +
Sbjct: 109 -GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELAQKT--DKSVWASLRARLS 165

Query: 123 FRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
             + +R A       LD + LT   NRPAG L++GQ++ LEI   +M  P++L+LDEP A
Sbjct: 166 GEQKDRIAQV-----LDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 220

Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242
           G+   ETE    L   L  +H  +++++EHDM  V SI+DH+ V++QG+ LA+G+ EQ++
Sbjct: 221 GMTDAETEFTAELFKSLAGKH--SLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQ 278

Query: 243 DNPEVIKAYLG 253
           DN  VI+ YLG
Sbjct: 279 DNERVIEVYLG 289


Lambda     K      H
   0.321    0.138    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 189
Number of extensions: 12
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 290
Length adjustment: 25
Effective length of query: 230
Effective length of database: 265
Effective search space:    60950
Effective search space used:    60950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory